Closed andreaniml closed 2 years ago
The scores really don't mean anything in this mode, so I wouldn't worry about it.
Looking at the clusters on a tree to see if you're happy with them, as it sounds like you are already doing, is a good idea. Minimum spanning trees can also sometimes be useful: https://poppunk.readthedocs.io/en/latest/mst.html
Thanks for the reply! The MST tree was useful too, thank you very much for the tip!
Hi! I'm sorry if this is a silly question
I'm dealing with closely related Salmonella (~3 different STs) and I am trying to fit a model to get an idea of the structure in my dataset (and possibly filter out some samples). I am trying to use the lineage mode using --rank 1,2,3,4,5,6 and my lineages seem to make sense (although there are some polyphyletic), however I'm unsure on how to know if I can trust this clusters or not.
From the documentation I get that the Score values are not that informative, but mine are really low, is this a problem?
My scores:
Many thanks!